Phylogenomics reveals the basis of adaptation of Pseudorhizobium species to extreme environments and supports a taxonomic revision of the genus
File(s)
Published version
Author(s)
Type
Journal Article
Abstract
The family Rhizobiaceae includes many genera of soil bacteria, often isolated for their association with plants. Herein, we investigate the genomic diversity of a group of Rhizobium species and unclassified strains isolated from atypical environments, including seawater, rock matrix or polluted soil. Based on whole-genome similarity and core genome phylogeny, we show that this group corresponds to the genus Pseudorhizobium. We thus reclassify Rhizobium halotolerans, R. marinum, R. flavum and R. endolithicum as P. halotolerans sp. nov., P. marinum comb. nov. , P. flavum comb. nov. and P. endolithicum comb. nov. , respectively, and show that P. pelagicum is a synonym of P. marinum . We also delineate a new chemolithoautotroph species, P. banfieldiae sp. nov. , whose type strain is NT-26 T (= DSM 106348 T = CFBP 8663 T ) . This genome-based classification was supported by a chemotaxonomic comparison, with increasing taxonomic resolution provided by fatty acid, protein and metabolic profiles. In addition, we used a phylogenetic approach to infer scenarios of duplication, horizontal transfer and loss for all genes in the Pseudorhizobium pangenome. We thus identify the key functions associated with the diversification of each species and higher clades, shedding light on the mechanisms of adaptation to their respective ecological niches. Respiratory proteins acquired at the origin of Pseudorhizobium were combined with clade-specific genes to enable different strategies for detoxification and nutrition in harsh, nutrient- poor environments.
Date Issued
2021-01-01
Date Acceptance
2020-11-11
Citation
Systematic and Applied Microbiology, 2021, 44 (1), pp.1-14
ISSN
0172-5564
Publisher
Elsevier
Start Page
1
End Page
14
Journal / Book Title
Systematic and Applied Microbiology
Volume
44
Issue
1
Copyright Statement
© 2020 The Author(s). Published by Elsevier GmbH. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)
License URL
Sponsor
Medical Research Council (MRC)
Identifier
https://www.sciencedirect.com/science/article/pii/S072320202030120X?via%3Dihub
Grant Number
MR/N010760/1
Subjects
Science & Technology
Life Sciences & Biomedicine
Biotechnology & Applied Microbiology
Microbiology
Rhizobium sp. NT-26
Genome taxonomy
Clade-specific genes
Ecological specialization
Phylogenomics
Pangenome analysis
Clade-specific genes
Ecological specialization
Genome taxonomy
Pangenome analysis
Phylogenomics
Rhizobium sp. NT-26
0603 Evolutionary Biology
0605 Microbiology
Microbiology
Publication Status
Published
Article Number
ARTN 126165
Date Publish Online
2020-12-15